Contacts of the helix formed by residues 320 - 331 (chain A) in PDB entry 5L0U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.3 4.8 - - - -
313A PRO 4.6 3.2 + - - -
314A VAL* 3.7 6.9 - - - +
315A LYS* 3.3 56.4 + - + +
319A SER* 1.3 79.4 + - - +
321A VAL* 1.3 65.1 + - - +
322A GLN 3.3 2.2 - - - -
323A GLU* 3.3 23.7 + - - +
324A LEU* 2.9 45.2 + - + +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.2 8.3 - - + -
224A LEU* 3.9 22.2 - - + -
232A VAL* 4.9 0.2 - - + -
269A PHE* 3.8 26.5 - - + -
291A PHE* 6.1 0.4 - - - -
314A VAL* 3.6 25.8 - - + -
318A LEU* 3.3 34.4 + - + +
319A SER 3.6 0.6 - - - -
320A ASN* 1.3 77.7 - - - +
322A GLN* 1.3 65.2 + - + +
324A LEU* 3.3 7.1 + - - +
325A LEU* 3.0 37.0 + - + +
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Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.9 28.3 - - + +
227A LYS* 4.3 12.5 + - - +
228A ASN* 5.2 4.6 - - - +
231A LEU* 3.9 29.6 - - + +
319A SER 5.2 1.2 + - - +
320A ASN 3.3 0.4 - - - -
321A VAL* 1.3 77.0 - - - +
323A GLU* 1.3 63.1 + - - +
325A LEU* 3.4 4.9 + - - +
326A GLN* 3.1 36.3 + - - +
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.8 13.3 - - + -
35A PHE* 3.8 30.3 - - + -
320A ASN* 3.3 23.3 + - + +
322A GLN* 1.3 79.4 - - - +
324A LEU* 1.3 56.6 + - - +
326A GLN* 3.4 11.4 + - - +
327A PHE* 3.0 27.1 + - - +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.8 25.1 - - + -
291A PHE* 3.9 14.1 - - + -
308A TRP* 3.8 25.1 - - + -
312A ILE* 3.9 9.0 - - + -
313A PRO 3.6 15.9 - - - +
314A VAL* 3.9 18.6 - - + -
320A ASN* 2.9 49.7 + - + +
321A VAL* 3.8 4.5 - - - +
323A GLU* 1.3 76.3 - - - +
325A LEU* 1.3 61.9 + - - +
327A PHE* 3.2 7.7 + - + +
328A VAL* 3.0 27.9 + - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER 5.6 0.2 - - - +
207A ALA* 4.0 14.4 - - + -
231A LEU* 4.0 29.8 - - + +
232A VAL* 4.0 22.4 - - + -
267A TYR* 3.9 25.4 - - + -
269A PHE* 4.8 1.1 - - + -
291A PHE* 3.8 26.2 - - + -
321A VAL* 3.0 38.0 + - + +
322A GLN 3.9 3.1 - - - +
323A GLU 3.3 0.2 - - - -
324A LEU* 1.3 74.6 - - - +
326A GLN* 1.3 63.2 + - - +
328A VAL* 3.3 3.9 - - - +
329A LYS* 3.1 35.7 + - - +
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS* 5.0 4.2 + - - -
32A TRP* 3.7 22.2 - - + -
231A LEU* 6.0 4.7 - - + -
322A GLN* 3.1 24.4 + - + +
323A GLU* 3.6 9.7 - - - +
325A LEU* 1.3 78.3 - - + +
327A PHE* 1.3 62.7 + - - +
329A LYS* 3.4 9.0 + - + +
330A ALA* 3.0 24.8 + - - +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.7 28.4 - - + -
35A PHE* 3.6 38.1 - + + -
36A ILE* 3.9 15.0 - - + -
39A ILE* 3.5 32.3 - - + -
308A TRP* 4.5 11.0 - + - -
312A ILE* 5.0 2.9 - - + -
323A GLU 3.0 14.7 + - - +
324A LEU* 3.2 10.1 + - + +
326A GLN* 1.3 76.9 - - - +
328A VAL* 1.3 76.5 + - + +
330A ALA 3.1 1.2 + - - -
331A ASN* 2.9 69.6 + - + +
334A VAL* 4.7 5.8 - - + -
335A ALA* 6.2 1.3 - - - -
338A ILE* 5.6 1.1 - - + -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.6 31.0 + - + -
289A LEU* 3.8 20.4 - - + -
291A PHE* 3.9 14.6 - - + -
312A ILE* 4.2 10.5 - - + -
324A LEU 3.0 13.4 + - - +
325A LEU* 3.3 17.9 - - - +
327A PHE* 1.3 92.4 - - + +
329A LYS* 1.3 65.6 + - - +
331A ASN 3.3 20.2 - - - +
332A ASP* 3.4 7.4 + - - +
335A ALA* 3.9 18.8 - - + +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER* 3.9 28.7 + - - -
230A LYS* 5.2 3.8 + - - +
231A LEU* 3.6 33.1 - - - +
267A TYR* 3.7 22.4 - - + +
325A LEU* 3.1 26.2 + - - +
326A GLN* 3.7 7.0 - - + +
327A PHE 3.2 0.2 - - - -
328A VAL* 1.3 78.2 - - - +
330A ALA* 1.3 59.3 + - - +
331A ASN 3.5 0.5 + - - -
332A ASP* 4.1 11.7 + - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.6 28.9 - - + +
326A GLN 3.0 16.9 + - - +
327A PHE 3.1 0.4 + - - -
329A LYS* 1.3 76.3 - - - +
331A ASN* 1.3 65.7 + - - +
332A ASP 3.8 1.3 - - - -
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Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 3.5 21.0 - - - -
36A ILE* 3.7 19.7 - - - +
327A PHE* 2.9 58.5 + - + +
328A VAL* 3.3 7.0 - - - +
330A ALA* 1.3 86.5 - - - +
332A ASP* 1.3 58.4 + - - +
333A ASP 3.3 2.9 - - - -
334A VAL* 3.3 15.2 + - + +
335A ALA* 3.0 23.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il